Structural Insights into Histone Demethylation by JMJD2 Family Members

Abstract

Posttranslational modifications of histones regulate chromatin structure and gene expression. Histone demethylases, members of a newly emerging transcription-factor family, remove methyl groups from the lysine residues of the histone tails and thereby regulate the transcriptional activity of target genes. JmjC-domain-containing proteins have been predicted to be demethylases. For example, the JmjC-containing protein JMJD2A has been characterized as a H3-K9me3- and H3-K36me3-specific demethylase. Here, structures of the catalytic-core domain of JMJD2A with and without alpha-ketoglutarate in the presence of Fe2+ have been determined by X-ray crystallography. The structure of the core domain, consisting of the JmjN domain, the JmjC domain, the C-terminal domain, and a zinc-finger motif, revealed the unique elements that form a potential substrate binding pocket. Sited-directed mutagenesis in conjunction with demethylase activity assays allowed us to propose a molecular model for substrate selection by the JMJD2 histone demethylase family.

Regulation of chromatin by histone modifications

“…One proline isomerase shown to act on histones is the yeast enzyme scFpr4, which isomerizes H3P38 [51]. This activity is linked to methylation of H3K36, presumably by scFpr4 affecting the recognition of K36 by the scSet2 methyltransferase and the scJMJD2 demethylase though the exact mechanism remains unclear [51,52]. Nevertheless, this example highlights the fact that proline isomerization is an important modification of the histone tail.…”

Structural insights into a novel histone demethylase PHF8

“…In addition, the levels of the other methylated histone peptides examined in this study remained unchanged (Supplementary information, Figure S1). To further confirm the demethylation, MALDI-TOF mass spectrometry was used to detect the change of the methylation state of histone peptides [4,5,18]. This protein exhibited demethylase activity toward the H3K9me2/me1 peptides, as npg indicated by the appearance of the peaks with mass of 3 264 and 3 250, which are 14 Da and 28 Da less than the original peptide (corresponding to loss of one and two methyl groups), respectively ( Figure 1C).…”

Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans

“…The crystal structure of LSD1 has been solved [38,[40][41][42] and the molecular determination for the sequence and methylation-state specificity has been uncovered. Although the structure of JMJD2A has been solved in apo form or in complex with its substrates [24][25][26][27], which provides insights into the molecular npg mechanism of catalysis and substrate recognition, how substrate specificity is determined for all other members of the JmjC domain-containing histone lysine demethylases remains to be elucidated.…”

“…Proteins in all of the seven groups have been demonstrated to be histone lysine demethylases, which remove methyl groups from histone H3 in a sequence-and methylation-state-specific manner [11][12][13][14][15][16][17][18][19][20][21][22][23]. The structures of JMJD2A, one of the JmjC domain-containing histone lysine demethylase specific for H3K9me3 and H3K36me3, have been solved in apo form or in complex with its substrates [24][25][26][27]. Although those structural studies had provided insight into the molecular mechanism of catalysis and substrate recognition, how substrate specificity is determined for most of the other JmjC domain-containing histone lysine demethylases was still unknown.…”